DNA
What is the difference between a pyrimidine and a purine? Give an example of each. What is the purpose of having these?
Pyrimidines are single ringed nucleotides. This is thymine and cytosine.
Purines are double ringed nucleotides. These include adenine and guanine.
They need to be this way so that the DNA can be antiparallel
DNA is read by DNA polymerase ____ to _____, but is synthesized _____ to _____.
DNA is read by DNA polymerase 3' to 5', but is synthesized 5' to 3'.
How is DNA polymerase different from RNA polymerase?
DNA polymerase requires a primer in order to bind, a RNA polymerase does not need a primer.
Where does translation occur?
In the cytoplasm with a ribosome, which is a massive structural protein, a riboprotein, where RNA components bind to tRNA
What are silent mutations? How do they affect protein synthesis?
When there is a change in a codon but you can't see a impact on the final product
Who contributed to figuring out the structure of DNA?
Watson, Crick and Franklin. There was a lot of information about DNA, they used that and Franklin’s x-ray diffraction image to identify the structure and building blocks of DNA.
Explain the difference between leading and lagging strands.
Leading: continuous and only has one primer
Lagging: have multiple RNA primers and continuously adds primers, creates okazaki fragments which are discontinuous stands added at the fork
Explain what happens during splicing.
Introns are removed and the exons are attached to one another for export from the nucleus to be made into proteins.
What does initiation look like when translating mRNA into a protein strand in eukaryotes?
The mRNA is bound to the small ribosomal subunit. The initiator tRNA with an anticodon (5’ CAU 3’) to match the codon (5’ AUG 3”) in the mRNA binds the mRNA.This tRNA is “charged” with a methionine amino acid. The large ribosomal subunit assembles on the complex putting the initiator tRNA in the P-siteAfter this, the initiator tRNA moves to the e-site and a new tRNA enters the a-site, continuing the cycle.
What are missense mutations? How do they affect protein synthesis?
When there is a change in an amino acid and it is not the original protein sequence coded from the DNA - there is an likely impact on the final product in which a different amino acid is placed, depending on the properties of the amino acid, it may not impact the final protein product
What was the experiment that Griffith performed and what did it contribute to the idea of DNA?
Determined there were two strains of pneumonia (virulent and avirulent)
Tested mice, injecting them with the S-strain (kill) and the R-strain (live). As well as the dead S-strain (live). He then decided to mix the living R-strains and dead S-strains and found that the rats still got sick and died.
There is a “transforming principle” and it’s probably in genetic material
Once the DNA is done replicating, what are three present problems that must be resolved?
DNA polymerase removes RNA primers using exonuclease activity
DNA polymerase fills gaps in DNA
Ligase: ties DNA back together, reforming phosphodiester bonds
What does initiation look like when making RNA in eukaryotes?
The TATA box is found and transcription factors bind which opens the DNA and recruits RNA polymerase
Describe the sites in a ribosome.
A-site: a charged tRNA binds to the mRNA in the ribosome
P-site: a peptide bond is formed between the growing chain in the P-site and the amino acid in the A-site
E-site: the tRNA leaves the ribosome
What are nonsense mutations? How do they affect protein synthesis?
When the change in nucleic acid results in a stop codon being created, meaning you get a shorter protein product.
What was the experiment that Avery, MacLeod and McCarty performed and what did it contribute to the idea of DNA?
They took a living S-strain, killed and purified the soluble portion. By using many enzymes determined that by removing certain enzymes that the only one that impacted “transforming” was the DNase
Contributing that DNA is the genetic material in S pneumonia
DAILY DOUBLE: 50 points for each of the 7 proteins that you can name that we went over and how they function to replicate DNA.
Helicase
Single-strand binding protein
Topoisomerase
Primase
DNA polymerase 3
DNA polymerase 1
DNA ligase
Describe the 3 things that must occur for mRNA to leave the cell?
Splicing, poly-A tail, 5’ cap. This matures the mRNA so it is able to be detected by ribosomes and does not degrade in the cytosol.
If the mRNA sequence was changed from: 5’ AUU GCG UCA UUA AGC 3’ to: 5’ AUA GCG UCC UUA AGU 3’, would it be a different protein sequence?
Ile-Ala-Ser-Leu-Ser
No
What are insertion or deletion mutations? How do they affect protein synthesis?
The nucleic acid change causes a frameshift and the codons from there on out are messed up, coding for a different sequence of amino acids.
What was the experiment that Hershey-Chase performed and what did it contribute to the idea of DNA?
Using radioactive labels in bacteriophage, they labeled proteins (sulfur) and DNA (phosphorus) and observed whether the phage ghost that left (the protein) was radioactive or the DNA left behind was
DNA is the genetic material NOT protein in T2 bacteriophage
Draw a replication bubble.
I don't want to pay for Jeopardy premium, so I will draw this on the board.
Transcribe the following DNA sequence and say it 5’ -> 3’:
Coding strand: 3’ C T T A C G T A A G T A 5’
Non-coding strand: 5’ G A A T G C A T T C A T 3’.
5’ A U G A A U G C A U U C 3’
Using this template DNA sequence: 5' ATC CGT TTC AAG 3' - determine the amino acid sequence.
mRNA 3' UAG GCA AAG UUC 5'
FLIPPED mRNA 5' CUU GAA ACG GAU 3'
Amino acid seq: Leu - Glu - Thr - Asp
If a missense mutation were to change a valine to an asparagine, how would this impact the protein in comparison to a change from valine to methionine?
The change from valine to asparagine is going from a nonpolar to a polar which would greatly impact the r-chain interactions. When compared to the change to methionine, it has a greater impact because the change to methionine is the same polarity as valine, likely impacting protein folding less.